Merge pull request #147 from henrypinkard/main

New major version of ndtiff python package

README.md

@@ -16,6 +16,29 @@ from ndtiff import Dataset
 data = Dataset('/path/to/data')
 ```
 
+or to write a new dataset:
+
+```python
+import numpy as np
+from ndtiff import NDTiffDataset
+
+summary_metadata = {'name_1': 123, 'name_2': 'something else'} # make this whatever you want
+dataset = NDTiffDataset('your/data/path', summary_metadata=summary_metadata, writable=True)
+
+image_height = 256
+image_width = 256
+
+for time in range(10):
+    # generate random image
+    pixels = np.random.randint(0, 2 ** 16, (image_height, image_width), dtype=np.uint16)
+
+    image_coordinates = {'time': time, 'other_axis_name': 4} # this can be whatever you want
+    image_metadata = {'name_1': 123, 'name_2': 'something'} # whatever you want
+    dataset.put_image(image_coordinates, pixels, image_metadata)
+
+dataset.finish()
+```
+
 ## Rationale
 The NDTiff library is optimized for size, speed, and flexibility. Several optimizations are in place to achieve high-performance in each category.
 

python/ndtiff/__init__.py

@@ -1,5 +1,7 @@
 name = "ndtiff"
 
+from ndtiff.ndstorage_base import NDStorageAPI, WritableNDStorageAPI
 from ndtiff._superclass import Dataset
 from ndtiff.ndtiff_dataset import NDTiffDataset
+from ndtiff.ndram_dataset import NDRAMDataset
 from ndtiff.ndtiff_pyramid_dataset import NDTiffPyramidDataset

python/ndtiff/_version.py

@@ -1,2 +1,2 @@
-version_info = (2, 3, 0)
+version_info = (3, 1, 0)
 __version__ = ".".join(map(str, version_info))

python/ndtiff/ndram_dataset.py

@@ -0,0 +1,67 @@
+from typing import List, Dict, Union
+
+import threading
+from ndtiff.ndstorage_base import WritableNDStorageAPI, NDStorageBase
+
+
+class NDRAMDataset(NDStorageBase, WritableNDStorageAPI):
+    """
+    A class for holding data in RAM
+    Implements the methods needed to be a DataSink for AcqEngPy
+    """
+
+    def __init__(self):
+        super().__init__()
+        self.images = {}
+        self.image_metadata = {}
+        self._finished_event = threading.Event()
+
+    def initialize(self, summary_metadata: dict):
+        self.summary_metadata = summary_metadata
+
+    def block_until_finished(self, timeout=None):
+        return self._finished_event.wait(timeout=timeout)
+
+    def finish(self):
+        self._finished_event.set()
+
+    def is_finished(self) -> bool:
+        return self._finished_event.is_set()
+
+    def put_image(self, coordinates, image, metadata):
+        key = frozenset(coordinates.items())
+        self.images[key] = image
+        self.image_metadata[key] = metadata
+        self._update_axes(coordinates)
+        self._new_image_event.set()
+
+    def get_image_coordinates_list(self) -> List[Dict[str, Union[int, str]]]:
+        frozen_set_list = list(self.images.keys())
+        # convert to dict
+        return [{axis_name: position for axis_name, position in key} for key in frozen_set_list]
+
+    #### ND Storage API ####
+    def close(self):
+        self.images = {}
+        self.image_metadata = {}
+        self.axes = {}
+
+    def has_image(self, channel=None, z=None, time=None, position=None, row=None, column=None, **kwargs):
+        axes = self._consolidate_axes(channel, z, position, time, row, column, **kwargs)
+        key = frozenset(axes.items())
+        return key in self.images.keys()
+
+    def read_image(self, channel=None, z=None, time=None, position=None, row=None, column=None, **kwargs):
+        axes = self._consolidate_axes(channel, z, position, time, row, column, **kwargs)
+        key = frozenset(axes.items())
+        if key not in self.images.keys():
+            raise Exception("image with keys {} not present in data set".format(key))
+        return self.images[key]
+
+    def read_metadata(self, channel=None, z=None, time=None, position=None, row=None, column=None, **kwargs):
+        axes = self._consolidate_axes(channel, z, position, time, row, column, **kwargs)
+        key = frozenset(axes.items())
+        if key not in self.images.keys():
+            raise Exception("image with keys {} not present in data set".format(key))
+        return self.image_metadata[key]
+